Powerful search tools in Windows & Mac

If you are an information worker (academic), having great support from powerful search tool is  crucial. Unless you have that sharp searching too, you will have trouble to pick that grain of information from the gigantic jungle of information coded in the form of data, sentences, or books.

There are great tools everywhere; but, some stand out in their capabilities than others.

The three giants in the Windows environment you might need to check are:

  1. Dtsearch (Windows)
  2. X1 search (Windows)
  3. Copernic desktop (Windows)
  4. FoxTrot Professional search (Mac)
  5. ? Devonthink (Mac)


Personally, I am not that much fond of Copernic mainly because it has no internal previewing tools; and, it seems to consume too much resource of my machine.

My number 1 pick is DtSearch. It is the best in its class in digging the tiniest of information. The proximity search is an invaluable tool to find associated ideas.

X1 comes closer. It is more of a document manager just like Devonthink in the mac than a specific searching tool. X1 also a wonderful application. It is cheaper than DtSearch.


As to FoxTrot, it is quite comparable to the DtSearch. But I like the preview system in FoxTrot even more.

The proximity search in DtSearch requires you to write the distances between the words(phrases) explicitly like Mary w/5 John (‘search Mary and John within the distance of 5 words’); while Foxtrot has a little scrolling window to search within a paragraph, within a sentence or less closer phrases.

One might put DT as a competitor to Foxtrot in the mac. But, I think FT is much superior on the search side while DT rocks for its AI and other organizational tools.

(Note, I don’t like giving links to the products because I don’t want to sound that I want to get a penny by associating them to my small, free, blog….I am dropping these notes because I believe these notes might help somebody out there; not because I have some other agenda. I used to keep these notes in my internal system; i put them out now in case somebody get sth useful out of these notes).


Mendeley vs Citavi vs Qiqq (also Sente and Bookends)

I haven’t used my Windows machine for a while now. I was then curious how the reference managers progressed in these periods. I was specially curious about Mendeley because I struggled with that application for some time then.

So, here is my observation: Mendeley stayed the same for the last couple of years. There is no real development; nor any change of any relevant sort since I knew the application. All the icons, the settings, the menus; the features: I see no changes. It is as clumsy as used to be; in many areas. One of the properties that Mendeley sucks at is how reference is downloaded from the internet. It attempts to use Google scholar; combining with its metadata extraction too. What it does is: it attempts to detect some DOI or other identifier to the PDF in the first few pages; and then, use that information to download reference information from Google scholars. For me, the result is a total debacle. It has always been a debacle. Mendeley can detect the papers only less than 5% of the times; as my PDFs don’t typically have metadata information; nor are they always published articles. Many of them are books; or drafts of books, and earlier versions of published articles I received from friends.

My favorite feature of Mendeley, which had been, still is: the BibTex sync feature. I have to admit, I have been tempted to live with Mendeley because of that feature. But, heck, if you have wicked reference data, what is the point of syncing it to Bib file. You will have incomplete citations ultimately. You will be embarrassed in front of colleagues when you realize that your references are incomplete after you sent out the paper. Because of the importance of the feature, I will focus on this feature in comparing the reference managers.

Citavis is not very far better than Mendeley when it comes to reference extraction from the internet. It can even be worse. I was able to download references from the internet only if the book has ISBN numbers or the article has DOI number. Otherwise, manual insertion is the only way I am left with. Look at this tutorial to learn how the process is clumsy in this application: https://youtu.be/MyaW9q_464w?list=PLkLfx87WKrTZTfifTvttqgKwzyQSTDYY5

In Citativ, when you read a PDF file, you can highlight or quote a certain text: comment on it; or give a short title to the comment and the quote. I totally love the idea of giving a short title to the quotation I make from a PDF reading. This feature is also available in Sente. The idea is: you quote a certain sentence or paragraph from the PDF; then, give a title which summarizes the core point of the quote and tag it if you want to. These quotes serve as a short summary of the article. The titles are your reminds of the core points of the quote. It is like summarizing the summary. Very neat approach to reading articles. The neat part in Sente is each of these short quotes could be exported as a separate note file. That means, if you have 20 quotations from the article, you will have 20 short notes: titled appropriately in a folder in finder. The problem with Citavi is each of the quotations are not exportable to separate notes. They can be exported as single file only. That means, it is not any better than reading and annotating a PDF in Acrobat Reader or other PDF readers (PDF exchange; or Foxit in windows: PDF expert in Mac)  and exporting a summary.

Qiqq is very different. Its way of extracting references from Google scholars is comparable to Sente. You click the PDF; click BibTex sniffer: you will be given Google scholars to pick the references. If Qiqq failed to detect the title of the PDF correctly, you can manually select the title. Qiqq immediately populates the scholar search with the selected text.

I have given the following book for all the three reference mangers: It was only Qiqq which correctly imported the full reference information.


I think the reference downloaded in Qiqq is much better than Sente. Sente has an advantage of downloading from multiple sources like WorldCat; Stanford, British libraries…very good results in some sources, weaker results in others. I used to get the most complete reference data from Stanford library website. But Sente sometimes fails to download the Publisher Field from many sources. Bookends can pick from Google Scholar, Justor and two other sources. But the process  of downloading a reference data (called Autocomplete in Bookends; targeted browsing in Sente; BibTex sniffing in Qiqq) is most elegant in Qiqq and Sente.


The other interesting feature of Qiqq is the brainstorming feature: absolutely brilliant tools to play with your references. It can also be used to track the positions one author took over time, how his/her ideas change in the long run. it can also be used to study the history of ideas: where a certain phrase appeared first; then, how other authors reflected that phrase in their publications. Look at these tutorials to see how the Brainstorming works in Qiqq:


My ratting of these reference manager’s capability of downloading references from the internet:

  1. Mendeley = 4/10
  2. Zotero= 3/10
  3. Citavi = 2/10
  4. Bookends = 7/10
  5. Sente = 9/10
  6. Qiqq = 8/10

Why is Sente higher in this ranking?

Because it offers much better choice than Qiqq on the sources. Qiqq does it elegantly on Google scholar; but, it cannot download from other sources which potentially offer more complete reference data.

Conclusion: if I ever have to move to Windows, I will definitely use Qiqq (in combination with OneNote or ConnectedText).

Boot windows uisng MiscroSD

Bootable MicroSD

I have a small netbook that failed to boot its operating system. I am trying to boot an XP operating system (downloaded as Iso file) using an 8GB MicroSD. I have tried many methods to produce bootable MicroSD. To mention the two:

1. Windows own tool to produce bootable operating system: it fails to load the Iso file, claims as not a valid iso file.

2. Manually formating the MiscroSD and trasfer the virual Drive (by virutally putting into drive) into the MSD: as explained in here (http://www.groovypost.com/howto/howto/create-a-windows-bootable-install-sd-card-or-usb-flash-drive/). This corrupted the MSD and failed to propertly format it. So, impossible to transfer the contents fo the virual disk

Final Solution–

1. Format the MiscroSD using advanced formatting tool ( https://www.sdcard.org/downloads/formatter_3/). You need to use the advanced formatting tool only if you have problem of formatting the disk, like I do.

2. Extract the contents of the iso file using 7zip

3. Burn the extracted contents of the iso file into the MiscorSD using WinToFalsh (http://wintoflash.com/download/en/)

Must have windows applications

Here, I will list some of the best windows application that, I presume, that every windows user “need” to have. Of course, there are a dozen of tech magazines and website that list a dozen of such stuffs. These sources can tell you all the powers that the applications can do, the features they come with. But, the writers of thee sources rarely tell you the actual experience they have with the applications. Yes, some many application these come crammed with so many great features. These so many features, however,  usually obscure the main objectives that the applications made for. That is what makes a pedantic application different from a usable application. Usability is what most tools lack these days. They cause you more confusion and annoyance than enjoyment and service.  Here, I will mention some of applications that I found to be more useful, based on my experience. Let me start from the academic tools

Academic Apps

LaTex (freeware) for writing your documents. If you have some serous academic paper to write, you have to get LaTex. But, for simple texts, stick with Microsoft Windows  or whatever text processing apps you have.

Notepad++(freeware) for text editing; TextStudio for LaTex documents; emacs/vim if you are a serous programmer.

Jabref: to manage your bibliography, if you are using Latex.

Mendeley Desktop to organize your PDF files: Currently there is no any alternative than mendeley to manage your pdf files. it is a great too. it can extract the metadata of the files, tag from Google Scholar, and even rename  and organize your files into groups.

PDF-Exchange to read PDF: you can also try Foxit. These two softwares are equally efficient for reading PDF files, though the former has more features in the free version than the latter.

Microsoft OneNote: for more serous notes. yes, Evernote is one of the greatest tools for clipping pages from websites and writing your own notes. But, after some practice and learning a lot about these two applications, I found OneNote to be better than Evernote, specially to write more serous notes. The way OneNote organizes the notes more intuitive and robust than Evernote. Now, it can also synchronize your note online (with SkyDrive).

Dropbox for your cloud computing needs. You already know it!

Calibre: to manage your ebooks. If you have e-reader like Nook or Kindle, the chances are you have a dozen of ebooks (EPub or Mobi) files. Calibre can help you to clean up the clutter. It can also convert from one format to the other. The best in the game!

Wordweb: desktop dictionary. No doubt, Wordweb is the most popular and the best dictionary application for windows. Lingoes is also great.

CutePDF: to convert your documents into PDF

Adobe Pro: to convert PDF files to other formats such as word, excel etc

Media Apps

MediaMonkey:for audio. MM is the best and probably the only software you need  to manage your music and audiobook. I know so many people use iTunes.  The main turn off for me with iTunes is the fact that it stores metadata about my files in a separate folder. That means, if you edit (tag) the name of the singer, the Album, the CD cover, all these information will be stored in iTunes library, not with your actual files. If you want to migrate to another application some time, you will lose all the editing you did on your files. You will not get the name of the artist, not the album…. That is bad. I want my files as clean and edited as I want. MediaMonkey can do it and store the information with the files. MediaMonkey also has better editing (tagging) tools than iTunes.

The KMPlayer: for videos. I know many people prefer VLC player. VLC is great for the fact that it can play almost all links of video/audio files you throw in to it. But, I found The KMPlayer more efficient in managing my video file. It can also play  all the popular video files.

Other Utilities

Google Chrome for browsing: I am sure you have already tried Chrome. it is a great  browser. It also seems a bit faster than Firefox.

UTorrent: small but efficient torrent downloader. you have to download the earlier version of uTorrent (2.1 or earlier)  if you what small size and efficient torrent downloader. The new versions have been damn shit!

IDM: for downloading files from internet: Internet download manager is  the fastest download manager in the market.  There are some other free alternatives to it. But, yah. I am not as such satisfied with them.

Revo Uninstaller: to uninstall applications. it removes all the junkie that uninstalled applications leave behind.

Ditto: to manage your clipboards. It keeps the contents you copied for latter use.

Everything: for desktop searching. Windows has its own desktop search engine. But, Everyting does the job faster. Switching off the search indexing of  the windows also helps your computer to perform  faster.

Directory Opus. Though  quite expensive, Opus is the best desktop explorer software. It has been two years since I used the regular explorer.

Avast free: for antivirus. Both avast and avira are great  antivirus programs. I prefer avast for two reasons. First, it doesn’t display adds ( Avira had been quite intrusive for some time. I am not sure right now if it still displays adds so aggressively as before). Secondly, it uses less resources than avira (in my pc)

Evernote: to clip webpages from website and write down notes.

7zip: to extract archive files: a free, fast  and powerful software! You get almost all the features of the expensive extractors such as winrar. Just wonderful!

Bulk Rename Utility: for renaming files, though its interface is ugly,  there is not better software than this one! It does the job very well

Tell me your favorite application!

Update: 2017-08-26

First, I am not using Windows that much any more. My daily computer is a 2012 macbook pro. But, I open my windows occasionally for some specific task.

Quite surprisingly, I am still sticking with most of the same tools that I have here. Only minimal changes.

  1. Google Chrome –> Opera. I have replaced Chrome with Opera because Opera is faster, less bulky and has free VPN. I still sometimes fire Chrome.
  2. Mendeley Desktop is removed for good. Zotero has gotten better. Qiqqa is even best. I was hopeful that Mendeley will be great. Over the years, my experience is, this application doesn’t change that much. It is a dead end, specially in heavily relied on Googld Scholar for metadata extraction.
  3. CutePDF: is no more necessary. There is default print to pdf service now.
  4. Directory Opus: is less required as the Windows own explorer has gotten much better these days. I am not using it that much anymore.
  5. Utorrent –> Qbittorent. I still have utorrent version 2.1; the last great utorrent. But, over the years, Qbittorent has gone much better. It has internal search ingine as well as downloader. It is free as well.
  6. Wordweb + Antidote: Now, I have one additional dictionary called Antidote. What is best about Antidote is that it can check grammar and correct spelling. It is more of a complete writing and editing system, alongside the dictionary. Very useful piece of software.
  7. Add a new search tool called dtSearch. I learned about this tool after searching for many search tools windows has to offer. I still use everything. But, dtsearch is in a different league. The most powerful searching tool in the Windows in existence. NO doubt.

Organize audio-books in iPod (iPhone) using MediaMonkey, the best method so far!

I LOVE audio-books. I enjoy listening them and learn a lot faster with them than reading. I usually listen  them in my leisure times, while doing some  physical exercise as in the gym, in the bus, while walking my ass …Winking smile. They are just great tools of learning; and  the iPhone (iPod) is a brilliant devise for audios. I also have Oxford & American Heritage dictionaries in it  to check out new words.  I know no other phone that has a better an application to manage audiobooks as well as great dictionary as Oxford and American Heritage. The main reason I bought the iPhone is of course for the audio-books.   

In this shallow world where substantive things lose value and triviality has got the utmost attention though, music has received more emphasis over audiobooks. Hence, Mr. Apple doesn’t take the case of audiobooks seriously in its devices. iPod is the perfect tool for music but not really as great as one expects for audio-books. There are a few tricks that you can do to get the books into the iPod; but not as such satisfactory specially when it comes to organization. I have tried different methods to organize my audio-books, to get each of the files in the books in a proper order so that listening would be more joy, organized and deductive. But, my frustration with ITunes was limitless. Spending hours and hours to make my audio-books easily accessible for  listening, I was not able to get all as I wanted. I have tried renaming the files, putting them into playlists, tagging track numbers etc. with no success.  The following two problems where specially annoying me all the time.

1. ITunes doesn’t allow importing many CDs of the same book as a single book.  If you want to get your audiobooks into your iPhone, you have to store them as music Albums. That is the trick you need to learn if you want to manage your books in iTunes.  But, storing audiobooks as music albums couldn’t give  you the flexibility to store different sections/chapters of the books as chapters/sections. I used to listen to an English vocabulary book called Verbal Advantage, as I mentioned before. The book has 24 CDS. I have to store each of the CDS as   separate books in the iPhone. This makes the ipod a total mess. While I had only about 90 audiobooks, the iPod actually used to display more than 300 audiobooks. That is just uncomfortable to browse the books. I want all the CDs as a single book. iTunes has a small trick thing to join the files of the CDs; I have used it for some time. But, that doesn’t work with mp3.

2. It Messes up track numbers: this is the terrible problem. In the middle of the listening, the the narration jumps from track 03 to 40. I have tried different methods to solve the problem in iTunes. Just terrible problems reappear now and then. 

I then discovered  MediaMonkey. It is not discovery actually. I have been using the software to manage music for about three years now. I can dare to say, MM is by far the best media  management software; and its tagging feature is  so incredible. I love it in all my heart. But, I was not able to get it work with my iPhone for some reason. Finally, I learned that the problem was related with QuickTime. Though there is not explicit requirement about the QuickTime, I found my iPhone failing to synchronize without it. So, I installed it beside iTunes. Everything works fine now. So, in this page, I will show you how you can exploit the powers of  MM to manage your audiobooks.

So, here is how I get the  best result in MM: 4 simple steps

1. Rename the files properly
2. Import them into MM
3. Tag the Title of the files from the file names
4. Remove the Track#
5. Voila!

1. The first step is  to properly rename your audio files. The renaming is necessary because tagging can be done from the name of the files. I use a software called Bulk Rename Utility to rename my files; an ugly, but so powerful software! it makes the renaming so simple. 

Just add some meaningful numbers as prefixes in the files, as

CD1-01 Introduction

CD1-02 ….



In this picture for example, I am simply prefixing CD7  on the existing names. The presix makes the iPod to arrange the files accordingly. The Bulk Renaming Utility (the book is “Verbal Advantage” as can you can see on the left side in the picture) can do complicated naming. You can add just prefixes, as I did here, Find and Replace, add numbers as Prefixes, etc.  This way of renaming, I will give your files a consistent file name that could  order them even if they are in the same folder. The file name also will function as the Title for the audio-files (as I will show you next). After prefixing the CD-numbers in each of the files,  I may then put all the files of the 24 disks into one folder(if I want to). Then

2. Import them into MM. I assume you know how the basics of MM. Go to Files->Add/Rescan files –>choose the folder where you have your audiobook; “[test]-Verbal Advantage” in my case. MM will import all the files in the folder.

3. Tag the files using the “auto-tag from file name” feature of MediaMonkey. Before you do the tagging, you have to select all the imported files of the book in MM. I selected all the files in the 24 CDs of the Verbal Advantage. You then go to Tools menu in MM and click on “auto-tag from file name”.  You will get a dialog box. In there, you will see the power of MM. It gives you the choices to tag Albums, Tracks, Artists etc from the file name. You can  specify to tag two or more features at the same time. But, for now, tagging the Titles of the audios from the filenames is quite sufficient. So, choose only <title> from the box and remove the others. MM will mark blue on the files that their Title is going to change.

Here is the screen- shot of the tagging window.  


The one I marked with red, for example, shows that the old Title “Introduction” is going to be replaced by a new title “CD-01-Introduction”. Click ok

4. Remove the Track# from the files. This is what motivated me to write this page today. Renaming and importing the files as I have described so far used to give me quite inconsistent results. For a reason I couldn’t explain, I sometimes used to get messed up orders of files in my iPhone. This morning, I discovered that the culprit is the Track# that the files come with. So, I have to remove it before I import the files into my iPhone. To do so, select all the files as usual –> right click –>properties . You will get a window. This is where you can insert the full metadata about your audiobook in MM. Here is what you have to do if you are not familiar with MM’s audiobook (music) management system.

a)  File path—leave it blank

b)  File Name—blank again

c)  Title –blank

d) Type: “audiobook” <—this is very important. your iPod will recognize the audiobook as  music otherwise. If you are using the older version of MM, you need to mark “audiobook” in the “Genre(s)” field.

e) Artist—write the artist(author) : “Charles Harrington Elster” in my case

f)  Track#: leave the box black, but tick the box in front of it. This will remove all the old track numbers stored in the files.


Note that deleting the track number is necessary only if you find it offending. If the the track numbers are properly set, they are great assets actually. So, the first thing is to try to synchronize the files to your iPhone and see of the order is good enough. If you find some files misplaced, say the 12th set as 2nd in the order, you need to go and remove the track number of those files (or from all the files). If you find the whole CDx (or a chunk of files) misplaced, probably, the Disk# is the culprit. So, go and remove (fix) it.

But, I have found one special advantage in removing track# totally from my files.  If the track#s are removed, the Titles (filenames) of the files  will be clearly visible in my iPod; otherwise, the iPod will be showing me only the track numbers (as 3 of 20). Being able to read the titles is actually good idea b/c you will be able to read in which chapter, section or subsection you are in, how the sections/chapters are organized enhancing your  comprehension; you can also easily skip the  chapter/topic that you are not interest in ; or just jump forth to the sections of your special interest. When I was listening  Bertrand Russel’s classic, “The History of Western Philosophy”, I had been skipping some of the sections about certain specific philosophers such as Hume and Descartes because I already heard (read) enough about them, targeting on less known ones helps me to get new ideas. The following picture is snapped from MM’s window. The names and numbers under Title column (marked Blue) will be visible in my iPhone. If I had no the Track# removed and hence  the Titles invisible in my iPod, I wouldn’t be able to see which section is about which philosopher, hence, forced to listen every section.


(You can, by the way, use an application called FlickTunes to supplement your Title reading experience in your iPod app. Search it in App Store.)

5. Transfer the files into your iPhone. Now, you have perfectly ordered files in your iPhone (iPod) stored as a single book. You don’t need to worry about jumping back and forth in the book; no clutter in your iPod; no hassling with playlists…. just play the first piece and enjoy your book to the end in one move!

Open-mouthed smileDelluOpen-mouthed smile

Organize audiobook in ipod (iphone) in Mediamonkey, best result

I LOVE audio-books. I enjoy listening them and learn a lot faster with them than reading. I listen them while doing some other physical work; as in the gym…they are just great tools of learning; and  an the iphone (ipode) is the best devise for audio. I know no other phone that has an application to manage audiobooks.  In this shallow world where substantive things lose value, music has got more emphasis over audiobooks. Hence, the Apple doesn’t take the case of audiobooks seriously in its devices. Ipod is good for music but not for audio-books. There is not good way of managing audio-books.

I have tried different methods to organize my audio-books. My frustration with Itunes was limitless. Spending hours and hours to make my audio-books easily accessible for easy listening had been so pain. The main problems were:

  1. Itunes doesn’t allow importing many CDs of the same book. If you want to get your audiobooks into your iphone, you have to store them as Albums. Storing audiobooks as music albums doesn’t give  me the flexibility to store different sections/chapters of the books as chapters/sections. I used to listen to an English vocabulary book called Verbal Advantage, as I mentioned before. The book has 24 CDS. I have to store each of the CDS as   separate books in the iphone. This makes the iphone a total clutter.
  2. it Messed up track numbers: this is the terrible problem. In the middle of the listening, the the voice jumps from track 03 to 40. I have tried playlists, renaming the files, properly tagging them. All didn’t work. just terrible problems reappear now and then.

I then shifted to MediaMonkey. I can dare to say, MM is the best media management software; and its tagging feature is  so incredible. But, you have to make sure that you installed itunes and  Quicktime for MM to work. Though there is not explicit requirement about the latter, I found my iphone failing to synchronize without it.

So, here is how I get the  best result in mediamonkey.

  1. First, you have to properly rename your audio files. The renaming is necessary because tagging can be done from the name of the files. I use a software called Bulk Rename Utility to rename my files; an ugly, but so powerful software! it makes the renaming so simple.

Here is how you can rename your files

CD1-01 Introduction

CD1-02 ….


In this picture for example, I am simply adding a prefix (CDx) in the Bulk Renaming Utility. This way, you will give your files a consistent file name that could  order them even if they are in the same folder. Then

  1. Import them into MM. I assume you know how the basics of MM.

  2. Tagg the files using the “auto-tag from file name” feature in mediamonkey. Before you do the tagging, you have to select all the imported files of the book in MM. You then go to Tools menu in MM and click on “auto-tag from file name”.  You will get a dialog box. In there, you have to specify what you are going to tag. Tagging the Titles of the audios from the filenames is quite sufficient. So, choose only <title> from the box. Let me, for example, show you how I tagged a 3CD book called  “Letting go of God” by Julia Sweeney. (don’t forget, I have renamed the files into CD1-01, CD1-02 etc. then, i have imported them; and selected all the files in the MM, then I am tagging them from the file names). So, here is the screen shot of the tagging process.

Reading inside Mendeley, better to avoid it

I have already started writing about the great research tool, Mendeley Desktop. I believe, mendeley is one of the mandatory tools every academician need to have. Many people are using it for many things. As to me, however, its main virtue is the ability to organize the actual PDF files in a brilliant manner. In this post, though, I am going to tell you why you need to avoid reading and annotating PDF files inside Mendeley itself.

If you are familiar with the fast and efficient PDF readers as Foxit and PDF-exchange, you will face too many constraints with Mendeley’s internal PDF reader, which I found to be unbearable. Of course, you can read, annotate and write notes inside mendeley. But, the main downside of Mendeley’s internal PDF reader is the fact that your annotations will be saved in separate folder. Mendeley has a system called database where it saves information about the PDF files. That database is in a different folder from the actual PDF files. Hence, if you open your Mendeley annotated PDF files in another PDF reader, you will not get the annotations. This is bad. I want my PDFs annotated wherever I open them, whenever I want.

Mendeley team has tried to alleviate the problem by adding a feature to export the annotations of the PDFs. But, I found this to be a laborious task. Should I open and export the annotations of each and every file every time I want to see my annotations in another software? no, I will not do it. So, if you are like me, the best approach is to manage your files inside Mendeley and read them using more potent PDf readers as Foxit. Your annotations and notes will be saved embedded inside the PDF files that you don’t have to worry opening them in another software.  You will enjoy your annotations to the  end of time (unless you want to remove them of course) wherever you go, which ever software you use.  So, to  open the files organized inside Mendeley with external readers, you have to right clicking the file and choose “Open file externally”. Your default reader will be fired. Voila!



Update: 2017-07-19

I don’t know that people still check  out this post. I wrote this in 2012.  I want to update  my latest experiences. I have given up with mendeley. I am now encouraging people to move away from this applicattion because the reference data it downloads is complete junk. The user has no option to download data from Woldcat or some other better source (national or international libraries; publishers like Jstor etc). I am now using am amazing reference manager called Bookends. Since I moved to Bookends, I am able to maintain a bigger, and clearer reference data.

Zotero is also a great tool.  For the peopl who use Latex, Jabref recently has grown extremely powerful reference manager. It has gone a lot of transformations. I highly encourage you to check out Jabref. Other great tool in the Windows is an application called Qiqqa. Citavi is also ok.  You can check out this post on the comparison of the other reference mangers.


Organize Mendeley’s Organizer using Duplicate File Detective

I have been using Mendeley Desktop for about two years now. Passing trough a lot of modifications, Mendeley Desktop has recently come out of its beta state. The best research project manager software now seems more stable and faster than ever.  Combing the potential of extracting the metadata of your PDF with the ability  organize and synchronize them with the cloud, no better application seem to exist that can satisfy all these needs.  Being a big fan of the application,  though, there are a few critical features that I am looking for implementation in its feature releases.  One of these is lack of Moving files while organizing files. If you use its file organization, it can only copy and rename  all the files in the library to a single folder. This means that, you should have a duplicate of files every time you use this feature. To alleviate this problem, I use an application called Duplicate File Detective. Of course, there are many duplicate removal applications out there. But, I prefer this application for one main reason; it can detect and delete only old versions of your files.

Here is how how to  do  it.

1. Open your Mendeley Desktop and make sure your  library as good as possible; Check the accuracy of the  metadata; check for duplicates in side Mendeley; check the dates, author, title of your files.

2.   After you make your library clean, go to Tools –>Option –>File Organizer. Check Organize my files. Click on Browse select a folder where you will store your whole library. You better select an empty ; otherwise, Mendeley will mix up your new files with the old files. You can also check Sort files into subfolders. But, I don’t recommend it. 


Check rename document files as the above picture, and finally Ok. This will copy all the files in your library to a folder (named AllLing in the picture). As you can see it I am also putting it in the dropbox folder. The reason is clear. Dropbox  gives more free cloud  space (2GB) than Mendeley (500MB). You can also get more free space by inviting your friends to it.

3. Since the above process copies all the files from their original folder to a new folder, you will have  two copies for each of your documents. To tackle this problem,  now you need to run Duplicate File Detective. In the DFD, select the disk where you store all your files and click Run Project.   When DFD finishes searching for duplicates, you will see all the duplicates in  a window. Go to Smart Mark (circled red in the picture below) –>mark Old files in Each Group –>Mark By File Created Date.


Now, give a glance on the list of files. If every thing is alright, all the old copies must be selected while the new copies stored in AllLing (in my case) remain unmarked. You can then either Move or Delete them. Now, you have cleared your clutter.

4. You can fix  a Watch Folder for Mendeley where you throw all new files that you will download from the internet. Mendeley will automatically import, extract the metadata , renamed and copy into  Organizer folder (AllLing in my case.).  After you make sure that the Mendeley has done its job, you can then manually delete the files in the Watch folder. 

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